Birth of the Pheonix
by F-14 Tomcat Lover
Summary: He was dishonored and broken. Lost and drowning in the seas of regret. Chairman Clyne gave him new hope and a new mission. Will Mark Owens avenge his disgrace of Junius Seven? Will he find his redemption or will he be forever a murderer?
1. Chapter 1

Disclaimer: I do not own Gundam SEED.

Summary: He was guilty of a crime without the hope of forgiveness, yet he was still spared, but barely. A year had passed and now the one upon whose grace had saved his life calls upon him. He had learned in prison what would happen if the others had their way. He knew that peace, which he alone shattered, must be rescued from those who only wish death.

**_"Birth of the Phoenix"_**

_**Phase One: "The Beginning of Redemption"

* * *

**_

**ZAFT military prison 210-K Block, Martius Four**

**February 6th, Year 71 of the Cosmic Era**

Twenty guards walked by the many different cells holding OMNI Enforcer POWs. Most looked injured and starved. The guards were not completely cruel, a few smuggled food into the many cellblocks to feed the hungry and medicine to treat the injured. They needed all the help they could get, but the sadistic commander believed what National Defense Chairman Patrick Zala said about Coordinators being a new race and that was how he got his posting. The twenty though were here with orders from the Council Chairman Sigel Clyne to get one prisoner. One who had been audibly praying for redemption for the horrid act he committed nearly a year ago. He had been the only one to live since he had not wanted that assignment, but still took the punishment.

Arriving at the cell and hearing the man pray for forgiveness from God, the guards opened the cell door. He did not stop; he did not waver. He continued and finished even as the guards began to lift him up and walk him out. The group of now twenty-one began to walk out of the prison. The prisoner did not even lift his head to look at any other prisoners. Their pain was all his fault or so he kept telling himself. He did not even face his escort. As they were about to leave, the warden who commanded the guards stepped forward to say a few things, but instead, the prisoner attacked him.

The guards tried to pull the man off of the warden. They couldn't, even though they were twenty and all Coordinators trying to pull one Natural off one more Coordinator. Only when the sound of a neck being broke did the guards finally remove him. The warden lay dead, his neck broken. The guards immediately began to return him to his cell, but a voice stopped them.

"No, we continue," Chairman Clyne said.

The guards looked to the First Generation Coordinator with something akin to shock, disbelief, and horror, among other looks all rolled into one. Still, they obeyed and the prisoner was brought out and escorted to a car where both the Chairman and the prisoner would ride with a small escort inside. The guards were very wary of the man being almost alone and in a confine space with the Chairman of the Supreme Council. Still they obeyed his orders and received orders to better care and treat the prisoners. Few felt indignant, but most were eager to follow it.

* * *

As the vehicle started towards the shuttle port, Chairman Clyne looked at the young man who still kept his head bowed. He saw a young man with his pride and honor stolen from him, ripped away like it was a part of his clothes or something, but went much deeper. Those two things had been more than clothe, a piece of him. When they were stolen, he might as well had an arm or leg stolen, but no one knew his pain. Sighing, he started to speak of his plans for the young man that would help him regain what he had lost.

"I've a plan for you that will help you regain what you lost," the man said nothing and did nothing.

"You will be made a commander of a new unit I intend to create out of POWs and volunteers," the man seemed to listen in closely.

"You will command a unit of Naturals and with divine hope, Coordinators," the man moved his head to listen better.

"The reason I chose you is simple. You have lost much and you seek redemption not only in the eyes of God or the people of the PLANTS, but of all of humanity, but you also know that it will be a long and hard journey. You are smart and brave; you still cling to the little remaining pride and honor you have left. With that in mind, I chose you, because you will never let another Junius Seven occur," the man lifted his head, but did not make eye contact.

"Your orders Commander are to enforce the laws governing warfare when ZAFT units break them. You are to command a team of your choosing and equip them however you want. You are also ordered and cleared to hunt down and destroy any and all Blue Cosmos Cells you come into contact. You are independent of the National Defense Committee and will report only directly to the Supreme Council. In short, you have been given a chance to redeem your pride and honor and forge new relations to prevent further war with the nations of Earth," the man was just a hair's breath from making eye contact.

"What did your old unit used to say? 'For the Preservation of Peace and Justice,' yes, a good saying and you shall return the peace lost by foolish radicals," the man established eye contact with a hopeful look in his eyes.

"Your first mission though is grave. I cannot believe that National Defense Chairman, Patrick Zala has lied to the council. The Alliance now has mobile suits; or rather one mobile suit is still left with-in its ranks. The pilot is said to be a Natural, but a spy has just informed me that the pilot is a Coordinator. I need proof so that we may begin negotiations again. You will have a letter to inform you of what is expected of you, but I believe it will fall well with-in your beliefs that you hold so dear. I pray that with men like you, that this war will come to a peaceful end," the man nodded and then spoke.

"Mission accepted sir, but why me… I know that my pride and honor has been my life, my life of dedicated service to the people of my nation no matter what their background, but I must still ask why me and not someone with less blood on their hands, especially innocent blood?" Chairman Clyne smiled.

"A man with a lesser tragedy wouldn't be able to carry out this mission to its full extent. There will be a lot more, naturally, since pirates and Alliance forces, for example mind you, will be in the way. I also need to know who actually permitted the development of those mobile suits with-in neutral space," the man didn't like that tone and phrasing.

"Sir, you mean a neutral state has fallen under ZAFT attack?" Chairman Clyne nodded and spoke.

"The Le Creuset Team attacked and destroyed Heliopolis. Five Alliance mobile suit prototypes had been built there with a warship to carry them. Now I've heard reports of three other mobile suits built there, but for the Orb Union that owned the colony. I also need the testimony of the Alliance crew or a refugee as that ship is carrying some aboard it. Zala refuses to let up the attacks and I'm afraid that the Eighth Lunar Fleet will be lost with its commander, Admiral Lewis Halberton," the man closed his eyes and took a deep breath.

"If I had to say who supported the Alliance R and D at Heliopolis, I would have to say it was either or actually, and most likely, both the Sahakus and the Seirans. They have always been problematic for the Athhas and Orb, as they want only power and prestige no matter whom they have to step on or go around," Chairman Clyne nodded believing what he said to be truthful.

"I take it they are not popular with in Orb?" the man nodded.

"The Sahakus think they are generals and nobles because they are born into a wealthy family. The Seirans are power hungry. If I had to come up with a way to create a sense of peace, I would say to marry a son of a powerful family here in the PLANTS to the daughter of the Athhas, but that is since you have a daughter and not a son," Chairman Clyne recognized the wisdom in that.

"I see, but alas that is not possible," the man nodded.

"Maybe, but I'm sure it is… You see I had a connection with-in GARM R and D, or rather a survivor who told me about the reality of the Mendel Colony attack by Blue Cosmos and I kept tabs on a young man that is connected to GARM R and D and his sister, too," Chairman Clyne leaned in to listen to more.

"The Ultimate Coordinator was in fact born, along with a, well I would have to say he isn't a carbon copy, so I'll call him a brother, more or less a half-brother," Chairman Clyne was surprised to say the least.

"His name is Kira Yamato and he might be that pilot you were talking about since he had moved with his adoptive parents to Heliopolis, while his sister was taken in by one Lord Uzumi Nara Athha… Cagalli Yula Athha," Chairman Clyne and the few guards were shocked.

"Neither knows that Ulen Hibiki and his wife Via had been their real parents. Obliviously for good reasons, damn good reasons. Since Blue Cosmos would go after both, though Yula Athha is a Natural through and through. It wouldn't matter to those zealots anyways," Chairman Clyne nodded to that.

"I will be your new commander under the condition that I get a mix force of my choosing and choice personnel of my choosing, but since you already agreed to that, I have one final condition," the man spoke dead serious.

"What is that condition?" Chairman Clyne hoped it wouldn't be too hard or something like that.

"Actually two, first though, I answer only to you or one of your allies," he said.

"I can see there will be a small problem, but I agree," Chairman Clyne knew he meant Sigel Clyne, not Chairman Clyne.

"Second and this one is more important then the first," he took a deep breath, "I want you to clean up the ZAFT POW situation. They left me alone because of you, but the others have not been so fortunate and when I say others, I mean the unilateral mistreatment of any Alliance Prisoner of War."

"I agree, that is more important and I will use my power to have Zala improve their conditions or I will remove the prisoner situation from his hands altogether," Chairman Clyne spoke agreeing to what he said.

"Then Commander Mark Owens at your disposal Chairman Clyne," he gave a poor ZAFT salute, but what was to be expected.

"Thank Commander Owens, you will have our latest ships and our latest mobile suits. You'll also have full autonomy and command authority, not to mention priority on the latest equipment. May you have a successful mission," Chairman Clyne shook the others hand.

* * *

**The Amafli Residence, Maius Four**

**February 17th, CE 71**

Nicol Amafli had just finished his shower when a maid called him down to the living room. Standing there were two men, one was the black uniformed captain of the _Vesalius_, Captain Jean Ades, and the other was a white uniformed commander with a nasty scar just under his right eye. Nicol saluted the two and noticed two females in green uniforms off to the side. Both held their duffel bags and each had a bag with a new uniform in it. Nicol was curious as to why a commander he never met was here with his ship's captain and two female green uniforms.

"Ah Nicol, glad you came right down, sorry to disturb you, but you've been reassigned from the Le Creuset Team," Captain Ades said, that was when Nicol noticed that Ades was acting strange.

"Where have I been transferred?" he asked, eyeing the new commander, he knew he recognized him from somewhere.

"To my team, Team Owens and I will be on the level, it is all volunteer, but its mission is classified at this time," Commander Owens spoke.

"I don't see a problem, but why is it classified?" Nicol asked.

"Since you have not stated that you will accept the transfer, you do not need to know," Commander Owens was serious.

"I… is there anything you can say?" he asked.

"Only this: my team is independent of ZAFT command and the National Defense Committee. We have priority on personnel and equipment and are being given the latest in the latter. Our mission is of the utmost seriousness and it is to ensure continued peace between the PLANTS and the nations of Earth," Commander Owens said.

"I and these two young ladies here are the first three he has seen and we have agreed. Nicol, trust me when I say this may very well ensure peace and will clean our records of the Heliopolis Tragedy," Captain Ades said.

"I still don't know, but I have a feeling that I won't regret it if I do join, so I will join the Owens Team," Nicol said.

"Very well, pack what you need and a few belongings, but leave your ZAFT red suits and flight suits behind as my team has a special uniform. You will be briefed aboard the _ZMS Soaring Sky_, my team flagship and that you will still be the pilot of the GAT-X207 Blitz. Thank you for accepting this posting Pilot Amafli," Commander Owens saluted Nicol and the others followed and Nicol returned it.

"I'll go pack now," and Nicol turned to leave.

"Pack for warm weather, we're heading to Earth and North Africa," Commander Owens called after him.

"Yes sir," Nicol called back.

* * *

**ZAFT Prison 32-C Block, Martius Five**

**Three hours later**

Six prisoners, four males and two females, were called out of their cells and escorted to the warden's office. No one liked to go there, few came back under their own power and some didn't come back outside of a body bag. When the six entered they found a different man sitting at the warden's desk. He rose to greet the six and had each take a chair. The prisoners noticed only a couple of guards, not the ten or twenty that were always around the old warden and these ones were new. Then the warden spoke to them.

"The old warden and some of his guards have been detained to answer for crimes against POWs," the six looked at him.

"I am now in charge of this prison facility, though it may not matter to any of you, because you six from C Block just might find yourselves leaving this place," the warden spoke directly and kindly in a way to each.

"What do you mean?" one of the males asked and a man in ZAFT Commander Whites stepped forward.

"Commander Owens here, needs a few good people to fill out his team and no he's not here to try and get you to join ZAFT. He is here to recruit you into a new unit that will be outside of even the National Defense Committee's control," the warden said.

"Say what?" another male prisoner asked.

"I'm a Natural like you, but I've taken some of the worst damage to be inflicted on a person and the result of my actions has placed you here. I need those who will fight for peace and justice. I need you to help create the peace that which has been shattered and to help forge relations to keep it in the post war years to come. I know some of the you may still cling to that propaganda nonsense that we had been told, but I am telling you here that we can truly make a difference in this war and in the times to come," Commander Owens said.

"You're that Owens, so why did they give you command?" a third male asked.

"_They_ didn't, Chairman Clyne did and only if I answered to him or a highly valued ally and that the conditions of the POWs improved. He agreed and I agreed, no more, no less," Commander Owens said.

"Fine, I agree," the third male said.

"I agree too, I can't stand being in those small cells much longer, I hate being in small areas," one of the females said.

"If may sister goes, I go," the other female said.

"Then I go too, because I will not stay here while others make a difference," the fourth male said.

"Why not," the first male said.

"I know I'm going to regret this, but I don't want to be here if things go bad, so yeah," the second agreed.

"Very good, gather what you have left and I'll meet you aboard my flag the _ZMS Soaring Sky_," Commander Owens saluted them, Alliance style.

They returned it and were escorted out to collect their remaining belongings and to get changed and transferred to the _Soaring Sky_, namesake of the _Soaring Sky_-Class that struck a startling resemblance to the _Archangel_-Class. Its general design was very much the same right down to the engines and weapons. The _Soaring Sky_-Class ships do have major differences though. Both catapults can be used to launch either mobile suits or mobile armor. Also, there is room for ten mobile suits and ten mobile armor in each ship. This though has also made the _Soaring Sky_-Class slightly larger than the _Archangel_-Class, but not by much and the use of space saving techniques was rigidly enforced so as to not make the new ships too large. They were also designed with atmospheric flight and amphibious sailing and submerging in mind that meant a stronger hull and engine design was required, plus re-entry capabilities and laminated armor to help with not only re-entry, but energy weapons as well.

* * *

**February 17th, CE**

**Supreme Council Chambers**

"What is going on?" demanded council member Orson White from Sextilis City.

"Indeed, I go home to visit see my wife and son and learn that Nicol has been transferred to a new unit and that unit isn't even on the official register," Councilman Yuri Amafli from Maius City said.

"On top of that the GAT-X207 Blitz and the captain of the _Vesalius_ were also transferred to this phantom unit," another councilman, Jeremy Maxwell from Quintilis City said as he broke his pen in two.

"There must be a reasonable explanation for all of this?" the cooler head of Councilwoman Ezalia Joule from Martius City said.

"I agree, but while were on the topic of oddities, when did POWs begin to concern the Administrative Committee?" asked Councilman Tad Elsman representing Februarius City PLANTS asked as he was a member of the Administrative Council.

"Since the National Defense Committee couldn't, and possibly wouldn't, reign in their wardens and guards and it might just be the same if handed over to the Judicial Committee so I chose to hand it over to a committee that deals with decisions like those all the time," Chairman Sigel Clyne and representing Aprilius City said.

"You do not trust the National Defense Committee then Chairman Clyne?" asked Councilman and head of the National Defense Committee Patrick Zala from December City PLANTS.

"To the point that I put Team Owens together, well I created the unit and chose its commander, but he put the team together," Chairman Clyne answered.

"Why did you do these things Chairman Clyne? I believe you owe an explanation," said October City representative Herman Gould, also of the National Defense Committee.

"I put this unit together and chose an Alliance officer to lead…" protests began at once, but surprising Councilwoman Joule called for silence and Chairman Clyne began again "… to lead this unit so that we could end the war sooner and diplomatically rather through force of arms. I also found, when considering this idea, that many ZAFT units were starting to get out of hand and so I decided that this unit would specialize in countering those problems and keeping units in line and preventing anymore Heliopolis battles as there is now evidence that only a few of Orb's government leaders and following back channels agreed to the construction of the five mobile suits. There is also evidence that Orb was producing its own mobile suits at Heliopolis and that program was government sanctioned. I had to ask myself if Commander Le Creuset truly knew that those mobile suits would go to the Alliance."

"Of course he knew and its been proven!" yelled Councilman Gould.

"Not true, actually, despite having the pictures from a spy in which we seen factory workers and mobile suits only, but no uniformed Alliance personnel. We also have no hard evidence even with the pictures of the 'Legged-Ship.' What we do know is after the battle began and not before even the infiltration of Le Creuset's commandoes. As such, those mobile suits and ship could have been built by and for the Orb military, even with the timely arrival of the Hawk of Endymion and an Alliance transport ship, it meant nothing, maybe a stop over to shelter themselves from Le Creuset for all he actually knew," the Chairman was quite prepared and showed the actual lack of evidence.

"So who is this Mark Owens? You said that he… NOT THAT MARK OWENS!" Louise Leitner from Junius City and member of the Judicial Committee yelled.

"Chairman Clyne you didn't?" Eileen Canaver from September City and one of Chairman Clyne's biggest supporters asked.

"The man who fired the nuclear missile that destroyed Junius Seven… Yes, I gave him command so that he may redeem himself not just to our eyes and that of every Coordinator, but to all the human race and himself. He still hardly ever establishes eye contact and tried to get out of commanding the new team, but in the end, for the transfer of the POWs care from the National Defense Committee so they could receive humane treatment and for him and his team to answer only to me or one other that I pick myself. He threw himself into forming this team, looking for the best and the brightest, but ones that were open minded about the whole affair. I even told him, my decision before hand that Naturals would be in the unit he commands. He was very careful about the selection. We had the ships and the equipment, but not the manpower. He choose only those that would fight for the Preservation of Peace and Justice, not the death of all Naturals or for a Pure and Blue World, which he told me he couldn't find a connection between Coordinator genetics and the environment, no matter how hard he tried. He seeks only to redeem himself and I have granted that to him. So let's see how things go, he allowed me to choose some personnel to keep watch over him," Chairman Clyne said.

"Yes, I see no problem and I agree that the National Defense Committee could have handled the POWs much more humanely. He also knows that with their new treatment, he must keep up his end. I say we trust him for now. After all, we all saw him that day over a year ago," Councilman Ali Kasim from Januarius City said.

**Flashback**

_A black with grey olive drab flight uniformed OMNI Enforcer TAS-2 Moebius mobile armor pilot was dragged into the council chambers of the Supreme Council of the Production Location on Ally Nexus Technologies, PLANT. There was a noticeable hole on the left sleeve where the unit insignia should be. It had been ripped off, though just from the flight suit, anyone could tell that the pilot was from the VF-728 Skull Squadron. Yet, that squadron was made up of strong willed and defiant pilots and support personnel, but this one looked broken, completely and utterly broken. _

"_Please don't hold my actions against my unit, please!" he begged._

"_Why not?" sneered Councilwoman Leitner._

"_My actions are my alone, they did not reflect upon the unit that I dishonored with the strike on Junius Seven. So PLEASE! Just punish me and leave them alone!" the man was begging as he cried for what he did._

"_You deserve more than what you will get you filthy Natural!" roared Councilman Gould._

"_Do you have any idea of what you have done?" asked Chairman Clyne._

"_I murdered nearly a quarter of a million people at the very least with a that missile and dishonored my former unit and my family name. Yes, I know what I did and would gladly sell my soul to prevent what I did, so that I alone would suffer," was the replied as the man never raised his head._

"_You should feel so lucky that we allow you to still breath and grace us with your pathetic presence," Councilman Zala said coldly and venom so powerful, it could melt a colony with one small drop._

"_I grace no one's presence because I am a murder. I should not receive pity or kindness for what I have done is inexcusable. I shouldn't even be given death nor allowed to live for the actions that I have caused to escalate this war from its onset. From here on out, millions will die and their blood shall cover my two hands and all because I am a murder that defines the word," the reply was as broken as the man._

"_Death will have to await you, for now you are Prisoner zero-zero-zero-one. Take him away," Chairman Clyne ordered despite the roars of protest from his fellows._

_As the man was taken away, he met eye contact with Councilwoman Ezalia Joule. He tried at once to break it, but the blue eyes seemed to be searching for something. They found what they had been searching for and the Councilwoman turned her head. No more than a split second had passed, but Councilman Kasim asked after the meeting what she had seen in Mark Owens' eyes. Her reply was simple and to the point._

"_He seeks redemption for what he has done, but has lost all hope for it," her reply made her wonder deeply about the man named Mark Owens._

"_He is not completely broken if he seeks redemption and that means there is still hope for him and that he does have hope. We shall see, but I believe the Chairman has a plan for him," Councilman Kasim said also curious about the man named Mark Owens._

**End Flashback

* * *

"Hmm… It will be interesting to see what he does. I shall give my consent for his team and its actions, provided they do nothing to harm the PLANTS," Councilwoman Joule said.**

The council almost unanimously agreed, save for three holdouts, Zala, Gould, and Leitner. The council continued to talk and agreed to announce the formation of Team Owens and its mission to the public. The Alliance and the PLANTS allies and the neutral nations, thus showing that the council was on top of things and planning to prevent future Heliopolis Incidents, would also hear this.

* * *

An hour later, aboard the _ZMS Soaring Sky_, the crew and pilots stood in the grayish blue and red uniforms of ZAFT style as Lacus Clyne shook the hands of each member of the ship's crew. As she went through the ranks, shaking each ones hands, she found that the Naturals and Coordinators tried to put some space between one another. She felt sad, but didn't show it and knew that some day this would be different. Then she came upon Commander Mark Owens and few people could forget his face. He stood there rigid, afraid to look into the face of Lacus Clyne. Until she took his hands and held them. He looked right into her smiling face and gave a weak smile himself. Cameras that had been showing live feed of the launch and of Lacus Clyne's send off, caught the small discussion between the man that killed a PLANT and the Pink Princess of the PLANTS.

"Ms. Clyne, next time you are anywhere near or visiting the memorial for the Junius Seven victims, can you say a few prayers for me and send my apologies to the victims. It isn't much, but I would like to do a little something, but I don't see my command being back anytime soon?" Commander Owens asked, pleading a hopeful dream.

"Yes Mr. Owens, I would be glad to send them your apology and pray for their souls for you. You are not a bad person by heart, but you did perform an evil deed that has been eating at your soul. Hopefully soon, you will be forgiven and able to stand proud like you used to before that black day," Lacus Clyne said, agreeing to his request and giving words of encouragement that seemed to help a little.

"Thank you Ms. Clyne, but now we must be on our way. We may be independent of ZAFT command, but we are still soldiers of ZAFT. We have to go and unfortunately fight in this terrible war," Commander Owens gave a proper ZAFT salute.

"I wish you and your team well commander and a safe and speedy journey home," the Pink Princess said as she and the camera crews boarded a shuttle to depart the _Soaring Sky_.

As the shuttle left, the _Soaring Sky_ and her five sisters, the _Thunder Cloud_, _Storm Chaser_, _Strong Winds_, _Highwind_, and _Air Burst_, sailed onto the start of their first mission. The path that led to the redemption of the flotilla's leader and the peaceful future that the crew sought.

* * *

Now this is something I know few, if any, have ever thought about. The man who destroyed Junius Seven is now the head of a ZAFT unit outside of ZAFT's control. The man seeks redemption and it will be curious to see how he does it. Also, more information related to the Owens Team's ships and mobile suits will appear in the next chapter. So, until then, please be patient and send in votes for pairings, because it is not decided whether or not this will be a truly canon take. 


	2. Apology

Disaster! I've recently suffered a mass loss of all my best chapters! It occurred with a computer crash. So I have to start practically all of my updates and new stories from scratch! TO all those who read my fan fiction, I am very sorry for this inconvenience and that it has happened at a time when I, myself, am moving and my newly acquired job is really starting to get busy. So don't expect updates any time soon, but rejoice that at least two update chapters were else where and are nearing completion.

The two Chapters are the following and so are their stories:

"**_Tale of a Lone Cat"_** – **Area 88**

**Arrival**

"**_In the Zone"_** – **Mobile Suit Gundam: SEED**

"**Battle of Heliopolis**

Also, I will be starting some new stories to hopefully help me back on track. I will also like to encourage anyone out there with some ideas for my next chapters and the ones that I'm going to be redoing to go ahead and contact me at my e-mail. I intend to make my stories more enjoyable, but I really am not good at thinking outside of a small circle of possibilities so I would like opinions and feedback to help to create more improved chapters and to those out there with a few secret tidbits of my stories, nothing will change, promise. That information is still highly accurate because I had written by hand those parts on line paper. So at least that information has not been lost. There will be, however, some slight changes, but only in the overall grand scheme of things.

Sincerely,

F-14 Tomcat Lover

Formerly Easy-Company-506/101, War-Reporter


End file.
